| Literature DB >> 29996561 |
Cara Mia Dunaiski1, Lena Janssen2, Hannah Erzinger3, Monika Pieper4, Sarah Damaschek5, Oliver Schildgen6, Verena Schildgen7.
Abstract
The molecular detection of Pneumocystis jirovecii is an important therapy-relevant tool in microbiological diagnostics. However, the quantification of this pathogen in the past has revealed discordant results depending on the target gene. As the clinical variety of P. jirovecii infections ranges between life-threatening infections and symptom-free colonization, the question arises if qPCRs are reliable tools for quantitative diagnostics of P. jirovecii. P. jirovecii positive BALs were quantitatively tested for the copy numbers of one mitochondrial (COX-1) and two nuclear single-copy genes (KEX1 and DHPS) compared to the mitochondrial large subunit (mtLSU) by qPCR. Independent of the overall mtLSU copy number P. jirovecii clustered into distinct groups based on the ratio patterns of the respective qPCRs. This study, which compared different mitochondrial to nuclear gene ratio patterns of independent patients, shows that the mtLSU gene represents a highly sensitive qPCR tool for the detection of P. jirovecii, but does not display a reliable target for absolute quantification.Entities:
Keywords: PCP; Pneumocystis jirovecii; quantification
Year: 2018 PMID: 29996561 PMCID: PMC6162491 DOI: 10.3390/jof4030084
Source DB: PubMed Journal: J Fungi (Basel) ISSN: 2309-608X
Results of the PneumoGenius® assay and the mtLSU PCR according to Botterell [14]. “+” positive tested, “⌀” negative tested.
| mtLSU | PneumoGenius® | mtLSU | PneumoGenius® | ||||
|---|---|---|---|---|---|---|---|
| mtLSU | DHPS | mtLSU | DHPS | ||||
| 1 | 2.52 × 105 | + | + | 26 | 6.48 × 103 | + | ⌀ |
| 2 | 7.55 × 104 | + | + | 27 | 2.45 × 106 | + | + |
| 3 | 1.36 × 106 | + | ⌀ | 28 | 1.05 × 106 | + | + |
| 4 | 1.38 × 106 | + | ⌀ | 29 | 3.12 × 106 | + | + |
| 5 | 4.41 × 104 | ⌀ | + | 30 | 4.15 × 106 | + | + |
| 6 | 3.22 × 105 | + | ⌀ | 31 | 7.84 × 106 | + | + |
| 7 | 4.02 × 104 | + | + | 32 | 7.50 × 104 | ⌀ | ⌀ |
| 8 | 2.20 × 102 | + | ⌀ | 33 | 1.95 × 105 | + | + |
| 9 | 1.21 | + | ⌀ | 34 | 2.21 × 106 | + | + |
| 10 | 9.26 × 106 | + | + | 35 | 2.22 × 106 | + | + |
| 11 | 7.63 × 106 | + | + | 36 | 3.36 × 104 | + | + |
| 12 | 1.12 × 106 | + | ⌀ | 37 | 8.76 × 106 | + | + |
| 13 | 4.52 × 106 | + | + | 38 | 2.87 × 106 | + | + |
| 14 | 6.92 × 103 | + | + | 39 | 1.08 × 106 | + | + |
| 15 | 1.02 × 104 | + | + | 40 | 1.00 × 106 | ⌀ | + |
| 16 | 5.71 × 105 | + | ⌀ | 41 | 6.73 × 106 | + | ⌀ |
| 17 | 9.77 × 106 | + | + | 42 | 1.65 × 106 | ⌀ | + |
| 18 | 4.33 × 105 | + | + | 43 | 2.78 × 105 | + | + |
| 19 | 1.52 × 106 | + | + | 44 | 2.60 × 106 | + | + |
| 20 | 1.43 × 105 | + | + | 45 | 1.55 × 105 | ⌀ | + |
| 21 | 3.19 × 103 | ⌀ | ⌀ | 46 | 4.29 × 106 | + | ⌀ |
| 22 | 4.60 × 103 | + | + | 47 | 1.12 × 103 | + | + |
| 23 | 1.58 × 104 | ⌀ | + | 48 | 1.42 × 104 | ⌀ | + |
| 24 | 3.77 × 103 | + | + | 49 | 8.35 × 103 | + | ⌀ |
| 25 | 9.27 × 103 | + | ⌀ | 50 | 6.92 × 103 | + | ⌀ |
Figure 1Copy number ratios of COX1, KEX1 and DHPS vs. the diagnostic relevant mtLSU gene in 29 BALF samples with high titer of mtLSU gene copies (≥ 1 × 107 mtLSU copies/mL). (a) Unsorted heatmap; (b) sorted heatmap; (c) According to their ratio pattern the samples were divided into seven clusters. In the clusters A and B only COX1 or DHPS were detected besides mtLSU, whereas in the clusters C and F DHPS or KEX1 are missing. In samples of the clusters D, E and G all target genes were detected, but each cluster displays a different ratio pattern.
Results of qPCRs for nuclear and mitochondrial gene copy number. Results of qPCRs for nuclear and mitochondrial gene copy numbers in 34 BALF samples with high titer of mtLSU gene copies (≥1 × 107 mtLSU copies/mL) before and after MACS purification of P. jirovecii particles. In case of samples 13, 18, 28, 29 and 31 no material was left for magnetic separation. After MACS purification of P. jirovecii particles three samples showed a positive fungal proof and two samples showed a positive bacterial proof in the respective endpoint PCRs. n/a not applicable.
| Sample No. | ||||||||
|---|---|---|---|---|---|---|---|---|
| Pre-Separation | Post-Separation | Pre-Purification | Post-Purification | Pre-Purification | Post-Purification | Pre-Purification | Post-Purification | |
| 1 | 4.33 × 108 | negative | 5.22 × 105 | negative | 1.21 × 106 | negative | negative | negative |
| 2 | 2.16 × 107 | negative | 5.93 × 103 | negative | negative | negative | negative | negative |
| 3 | 9.02 × 108 | 1.30 × 107 | 3.33 × 109 | 3.14 × 108 | 2.08 × 108 | 2.19 × 109 | 9.97 × 108 | 7.04 × 107 |
| 4 | 9.52 × 107 | 3.30 × 104 | 1.53 × 106 | 1.82 × 105 | 1.30 × 107 | negative | 7.41 × 105 | negative |
| 5 | 7.99 × 109 | 2.20 × 105 | 8.12 × 1010 | 5.18 × 107 | 3.77 × 109 | 1.40 × 108 | 2.04 × 1010 | 9.44 × 106 |
| 6 | 1.99 × 109 | 8.20 × 104 | 1.56 × 107 | 1.14 × 106 | n/a | negative | 5.21 × 105 | 2.73 × 101 |
| 7 | 3.50 × 107 | negative | 1.36 × 105 | negative | n/a | negative | 1.30 × 104 | 4.22 × 103 |
| 8 | 2.62 × 107 | negative | 6.56 × 104 | 9.51 × 104 | 1.47 × 104 | negative | 4.71 × 105 | negative |
| 9 | 2.33 × 109 | 6.20 × 104 | 4.79 × 101 | negative | negative | negative | negative | negative |
| 10 | 1.47 × 108 | negative | negative | negative | negative | negative | 2.54 × 103 | negative |
| 11 | 2.11 × 109 | 1.70 × 1011 | 6.26 × 105 | 1.89 × 105 | negative | negative | 2.16 × 104 | negative |
| 12 | 5.79 × 108 | negative | negative | negative | negative | negative | negative | negative |
| 13 | 3.32 × 1012 | n/a | 1.49 × 1010 | n/a | 2.05 × 1010 | n/a | 2.52 × 1013 | n/a |
| 14 | 1.03 × 1010 | 1.30 × 107 | 1.37 × 109 | 1.75 × 109 | 1.84 × 109 | 8.41 × 109 | 1.00 × 1011 | 4.04 × 109 |
| 15 | 1.13 × 108 | negative | negative | negative | negative | 5.71 × 107 | negative | negative |
| 16 | 4.33 × 109 | negative | negative | negative | negative | negative | negative | negative |
| 17 | 5.99 × 108 | 3.60 × 1011 | 4.52 × 105 | 2.90 × 104 | 2.06 × 105 | negative | negative | negative |
| 18 | 1.61 × 1014 | n/a | 1.14 × 109 | n/a | 5.04 × 109 | n/a | 3.04 × 107 | n/a |
| 19 | 1.59 × 1010 | 1.40 × 106 | 4.20 × 108 | 2.22 × 108 | 3.24 × 109 | 9.40 × 108 | 2.59 × 107 | 2.25 × 108 |
| 20 | 2.70 × 107 | 2.10 × 102 | negative | negative | negative | negative | negative | negative |
| 21 | 2.98 × 1011 | 8.60 × 106 | 3.05 × 1011 | 1.03 × 109 | 6.45 × 1010 | 9.55 × 109 | 1.53 × 1011 | 7.11 × 109 |
| 22 | 1.05 × 1012 | 1.90 × 106 | 2.74 × 108 | 1.96 × 108 | 8.51 × 109 | 9.07 × 108 | 6.29 × 107 | 3.14 × 108 |
| 23 | 1.01 × 1011 | 3.50 × 107 | 1.44 × 1010 | 4.82 × 108 | 2.52 × 109 | 5.89 × 108 | 3.91 × 109 | 3.47 × 106 |
| 24 | 9.92 × 108 | 4.00 × 1014 | negative | negative | negative | negative | negative | 1.21 × 104 |
| 25 | 2.11 × 107 | 3.70 × 105 | 1.67 × 106 | 8.37 × 104 | negative | negative | 2.34 × 105 | negative |
| 26 | 1.09 × 1010 | 6.50 × 108 | 2.17 × 1011 | 1.05 × 1010 | n/a | 5.64 × 1010 | n/a | 2.25 × 109 |
| 27 | 1.65 × 108 | negative | 3.24 × 104 | negative | negative | negative | 1.11 × 104 | 9.39 × 103 |
| 28 | 1.07 × 108 | n/a | 5.92 × 107 | n/a | 5.23 × 106 | n/a | 2.39 × 107 | n/a |
| 29 | 1.04 × 109 | n/a | 1.17 × 1010 | n/a | 6.56 × 108 | n/a | 1.55 × 109 | n/a |
| 30 | 2.88 × 107 | 5.70 × 103 | negative | negative | negative | negative | negative | 4.66 × 103 |
| 31 | 1.79 × 107 | n/a | negative | n/a | negative | n/a | 4.83 × 103 | n/a |
| 32 | 9.90 × 108 | negative | 1.21 × 106 | negative | 7.41 × 105 | negative | 3.79 × 106 | negative |
| 33 | 2.80 × 108 | negative | 6.20 × 104 | negative | negative | negative | negative | 2.08 × 104 |
| 34 | 1.98 × 1010 | 6.20 × 105 | 1.21 × 106 | 5.00 × 106 | 7.41 × 105 | 2.66 × 107 | 3.79 × 106 | 2.85 × 106 |